Index

A

addKineticFxnsToPath() (in module ensembleFxns)

aggregate_time_series() (in module simulation_viz.import_simulation_data) algebra() (in module patternFxns)

B

buildAllosteric() (in module patternFxns) buildDiffusion() (in module patternFxns) buildEnsemble() (in module ensembleFxns) buildFixedExchange() (in module patternFxns)

buildFreeExchange() (in module patternFxns) buildKineticFxn() (in module patternFxns) buildMassAction() (in module patternFxns) buildOdeFxn() (in module patternFxns) buildReaction() (in module patternFxns)

C

calculate_dG() (in module simulation_viz.process_thermodynamics) calculateExtremePathways() (in module patternFxns) calculateKineticParams() (in module patternFxns) check_for_negative_concentrations() (in module simulation_viz.check_simulations) checkStability() (in module ensembleFxns) colVector() (in module patternFxns)

computeBranchedReversibilities() (in module patternFxns) computeGibbsFreeEnergyRanges() (in module ensembleFxns) computeRobustFluxes() (in module ensembleFxns) controlAnalysis() (in module analysisFxns) controlAndResponseAnalysis() (in module analysisFxns) cycledPaths() (in module patternFxns)

E

ensembleStabilityTest() (in module analysisFxns)

exportSBML() (in module ensembleFxns) extractPrior() (in module ensembleFxns)

F

findIssuesWithTMFA() (in module ensembleFxns)

fixVariableNames() (in module ensembleFxns)

G

gather_conc_data() (in module simulation_viz.import_simulation_data) gather_flux_data() (in module simulation_viz.import_simulation_data) generalHR() (in module ensembleFxns) get_fluxes_and_dGs() (in module simulation_viz.process_thermodynamics) get_met_rxn_names() (in module simulation_viz.import_simulation_data)

get_non_converging_models() (in module simulation_viz.check_simulations) get_robust_fluxes() (in module simulation_viz.process_thermodynamics) get_time_series_quartiles() (in module simulation_viz.import_simulation_data) getExpression() (in module patternFxns) getLink() (in module patternFxns) getWeight() (in module patternFxns)

I

import_ref_conc() (in module simulation_viz.import_simulation_data) import_ref_flux() (in module simulation_viz.import_simulation_data)

initializeEnsemble() (in module ensembleFxns) initialSampler() (in module ensembleFxns)

L

load_simulation() (in module simulation_viz.import_simulation_data)

loadEnsembleStructure() (in module ensembleFxns)

M

module simulation_viz.check_simulations simulation_viz.import_simulation_data simulation_viz.process_thermodynamics simulation_viz.visualize_simulations, [1] simulation_viz.visualize_simulations_interactive

P

plot_ensemble() (in module simulation_viz.visualize_simulations), [1] plot_ensemble_interactive() (in module simulation_viz.visualize_simulations_interactive) plot_model() (in module simulation_viz.visualize_simulations), [1]

plot_model_interactive() (in module simulation_viz.visualize_simulations_interactive) plotControlAnalysis() (in module analysisFxns) plotControlAndResponseAnalysis() (in module analysisFxns) poolConstraintFxn() (in module ensembleFxns)

R

reactionPattern() (in module patternFxns)

readInput() (in module patternFxns) remove_models() (in module simulation_viz.check_simulations)

S

sampleAllostery() (in module ensembleFxns) sampleEnzymeAbundances() (in module ensembleFxns) sampleFluxesAndGibbsFreeEnergies() (in module ensembleFxns) sampleGeneralReversibilities() (in module ensembleFxns) sampleModifierElemFluxes() (in module ensembleFxns) simulateEnsemble() (in module analysisFxns) simulation_viz.check_simulations module

simulation_viz.import_simulation_data module simulation_viz.process_thermodynamics module simulation_viz.visualize_simulations module, [1] simulation_viz.visualize_simulations_interactive module